Question 1

Imagine a protein that can be independently phosphorylated on any of its 10 tyrosine residues and acetylated on either of its 2 lysine residues. In principle, how many different combinations of these modifications are possible for this protein?

Accepted Answer

Each modification can have two different states, which therefore doubles the number of combinations.

Question 2

The structural formulas for the 20 naturally occurring amino acid residues are shown in the panel below. Answer the following question(s) with the help of this panel.
 
-Which of the amino acids shown above has the most limited combinations of phi (?) and psi (?) angles in its Ramachandran plot? Write down the one-letter abbreviation for it, e.g. A.

Accepted Answer

Proline, being an imino acid, can adopt only a limited set of configurations within a polypeptide chain.

Question 3

A protein is drawn in the following simplified diagram undergoing a set of covalent modifications including the addition of a chain of ubiquitin protein monomers (U) to one of its lysine side chains, a phosphate moiety (P) to its tyrosine side chain, and a lipid farnesyl (F) to its cysteine side chain. Indicate the order of these modifications (1 to 3) in the diagram. Your answer would be a three-letter string composed of letters F, U, and P only, e.g. PFU.
  
Answers

Accepted Answer

Attachment of lipid compounds such as the farnesyl group to a protein causes it to become membrane-associated. At the right time, a specific phosphorylation can result in recognition of the protein by certain partners, which in this case target the protein for degradation by polyubiquitin addition.
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Question 4

The structural formulas for the 20 naturally occurring amino acid residues are shown in the panel below. Answer the following question(s) with the help of this panel.
 
-What is the amino acid sequence of the peptide depicted below? Write down the sequence from the N- to the C-terminus, and use only the one-letter abbreviations, e.g. AGCNT.

Accepted Answer

The sequence is cysteine-glutamic acid-leucine-leucine.

Question 5

In an ? helix, each amino acid residue is rotated by about +100° and raised by about 0.15 nm relative to the previous residue. This means that each full turn of the helix rises by … nm parallel to the helix's axis.

Accepted Answer

A full (360°) turn in the ? helix contains 3.6 residues (360°/[100° per residue]), and is thus raised by 0.54 nm:
3.6 residues per turn × 0.15 nm rise per residue = 0.54 nm rise per turn.

Question 6

Imagine that 1 L of a solution containing each of the 20 naturally occurring amino acids at 50 mM concentration each (total concentration of 1 M) is allowed to polymerize in a perfectly stepwise fashion such that at each step, a random amino acid can be incorporated into a growing polypeptide. The steps are repeated, until eventually the solution is only composed of 40-mers (and virtually all of the monomers have been used). What fraction of all 40-mers can possibly be present in this solution? Round your number to four decimal places. Avogadro's number is 6 × 10²³.

Accepted Answer

The number of possible 40-mers is equal to 20?? or approximately 10?². If every 40-mer in the solution has a unique sequence, there will be 0.025 moles of different 40-mers made in this solution (since the total amount of monomer was 1 mole), which is equivalent to 1.5 × 10²² molecules. Thus, only about one out of every 10³? possible 40-mer peptides has been sampled in this solution. Even the whole universe does not have enough atoms to sample all possible sequences for a protein with 300 amino acid residues in this way.

Question 7

For a simple enzymatic reaction that involves only one substrate and follows Michaelis-Menten kinetics, the changes in the concentrations of substrate, product, free enzyme, and the enzyme-substrate complex over the course of the reaction are depicted by solid curves in the graph below. Which curve (1 to 4) corresponds to [ES]? Write down the number as your answer.

Accepted Answer

After a brief initial period of pre-steady state, the concentration of the formed ES complexes remains more or less constant in the apparent steady-state phase. This assumption allows the derivation of the Michaelis-Menten equation for reaction rate that involves Vm??, Km, and [S].

Question 8

The structural formulas for the 20 naturally occurring amino acid residues are shown in the panel below. Answer the following question(s) with the help of this panel.
 
-What is the amino acid sequence of the peptide depicted below? Write down the sequence from the N- to the C-terminus, and use only the one-letter abbreviations, e.g. AGCNT.

Accepted Answer

The sequence is serine-cysteine-isoleucine-glutamic acid-asparagine-cysteine-glutamic acid.

Question 9

A simple protein interaction map is shown below for human cytochrome c (Cyt), a heme-containing protein that is normally found inside the mitochondria and is associated with the electron-transport chain (ETC) of the inner mitochondrial membrane. Under special emergency conditions, this protein can also moonlight as a signal transducer for the onset of a pathway leading to programmed cell death (PCD). As shown in the map, it also interacts with a group of phosphoprotein phosphatases (PPP) involved in cell signaling pathways. Assuming that the functions of the proteins labeled as X, Y, and Z are unknown, which of the following points can be reasonably argued from this interaction map?

Accepted Answer

Just because two proteins closely interact with each other, it does not mean that they have the same enzymatic activity. For example, a scaffold protein is generally expected to interact with many of the subunits in a complex. Proteins that display similar patterns in maps derived from different organisms are likely to have similar functions-almost certainly if they also have homology. Note that such a map only shows the small subset of interactions from the whole organism that are clustered around cytochrome c, and does not reflect all of the interactions for all of the proteins shown.

Question 10

Some protein domains are found in many different proteins and have been especially mobile during evolution. A domain of this kind is called a "protein …"

Accepted Answer

Protein modules are a subset of protein domains that have been especially mobile during evolution and seem to have particularly versatile structures.

Question 11

The structural formulas for the 20 naturally occurring amino acid residues are shown in the panel below. Answer the following question(s) with the help of this panel.
 
-What is the amino acid sequence of the peptide depicted below? Write down the sequence from the N- to the C-terminus, and use only the one-letter abbreviations, e.g. AGCNT.

Accepted Answer

The sequence is that of the mammalian peptide hormone vasopressin: glycine-arginine-proline-cysteine-asparagine-glutamine-phenylalanine-tyrosine-cysteine. Note the disulfide bond between the two cysteines.

Question 12

The structural formulas for the 20 naturally occurring amino acid residues are shown in the panel below. Answer the following question(s) with the help of this panel.
 
-Which amino acid residues shown above have acidic side chains? Write down the one-letter abbreviations for them, in alphabetical order, e.g. ACGNV.

Accepted Answer

Aspartic acid and glutamic acid residues have acidic side chains, and are usually negatively charged in cellular proteins.

Quiz 3: Proteins

Imagine a protein that can be independently phosphorylated on any of its 10 tyrosine residues and acetylated on either of its 2 lysine residues. In principle, how many different combinations of these modifications are possible for this protein?

In an ? helix, each amino acid residue is rotated by about +100° and raised by about 0.15 nm relative to the previous residue. This means that each full turn of the helix rises by … nm parallel to the helix's axis.

Some protein domains are found in many different proteins and have been especially mobile during evolution. A domain of this kind is called a "protein …"